1
|
Wu HYL, Jen J, Hsu PY. What, where, and how: Regulation of translation and the translational landscape in plants. THE PLANT CELL 2024; 36:1540-1564. [PMID: 37437121 PMCID: PMC11062462 DOI: 10.1093/plcell/koad197] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/04/2023] [Revised: 06/14/2023] [Accepted: 06/15/2023] [Indexed: 07/14/2023]
Abstract
Translation is a crucial step in gene expression and plays a vital role in regulating various aspects of plant development and environmental responses. It is a dynamic and complex program that involves interactions between mRNAs, transfer RNAs, and the ribosome machinery through both cis- and trans-regulation while integrating internal and external signals. Translational control can act in a global (transcriptome-wide) or mRNA-specific manner. Recent advances in genome-wide techniques, particularly ribosome profiling and proteomics, have led to numerous exciting discoveries in both global and mRNA-specific translation. In this review, we aim to provide a "primer" that introduces readers to this fascinating yet complex cellular process and provide a big picture of how essential components connect within the network. We begin with an overview of mRNA translation, followed by a discussion of the experimental approaches and recent findings in the field, focusing on unannotated translation events and translational control through cis-regulatory elements on mRNAs and trans-acting factors, as well as signaling networks through 3 conserved translational regulators TOR, SnRK1, and GCN2. Finally, we briefly touch on the spatial regulation of mRNAs in translational control. Here, we focus on cytosolic mRNAs; translation in organelles and viruses is not covered in this review.
Collapse
Affiliation(s)
- Hsin-Yen Larry Wu
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI 48824, USA
| | - Joey Jen
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI 48824, USA
| | - Polly Yingshan Hsu
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI 48824, USA
| |
Collapse
|
2
|
Bernal-Gallardo JJ, de Folter S. Plant genome information facilitates plant functional genomics. PLANTA 2024; 259:117. [PMID: 38592421 PMCID: PMC11004055 DOI: 10.1007/s00425-024-04397-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/11/2024] [Accepted: 03/20/2024] [Indexed: 04/10/2024]
Abstract
MAIN CONCLUSION In this review, we give an overview of plant sequencing efforts and how this impacts plant functional genomics research. Plant genome sequence information greatly facilitates the studies of plant biology, functional genomics, evolution of genomes and genes, domestication processes, phylogenetic relationships, among many others. More than two decades of sequencing efforts have boosted the number of available sequenced plant genomes. The first plant genome, of Arabidopsis, was published in the year 2000 and currently, 4604 plant genomes from 1482 plant species have been published. Various large sequence initiatives are running, which are planning to produce tens of thousands of sequenced plant genomes in the near future. In this review, we give an overview on the status of sequenced plant genomes and on the use of genome information in different research areas.
Collapse
Affiliation(s)
- Judith Jazmin Bernal-Gallardo
- Unidad de Genómica Avanzada (UGA-Langebio), Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional (Cinvestav), Irapuato, Mexico
| | - Stefan de Folter
- Unidad de Genómica Avanzada (UGA-Langebio), Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional (Cinvestav), Irapuato, Mexico.
| |
Collapse
|
3
|
Wu TY, Li YR, Chang KJ, Fang JC, Urano D, Liu MJ. Modeling alternative translation initiation sites in plants reveals evolutionarily conserved cis-regulatory codes in eukaryotes. Genome Res 2024; 34:272-285. [PMID: 38479836 PMCID: PMC10984385 DOI: 10.1101/gr.278100.123] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2023] [Accepted: 02/15/2024] [Indexed: 03/22/2024]
Abstract
mRNA translation relies on identifying translation initiation sites (TISs) in mRNAs. Alternative TISs are prevalent across plant transcriptomes, but the mechanisms for their recognition are unclear. Using ribosome profiling and machine learning, we developed models for predicting alternative TISs in the tomato (Solanum lycopersicum). Distinct feature sets were predictive of AUG and nonAUG TISs in 5' untranslated regions and coding sequences, including a novel CU-rich sequence that promoted plant TIS activity, a translational enhancer found across dicots and monocots, and humans and viruses. Our results elucidate the mechanistic and evolutionary basis of TIS recognition, whereby cis-regulatory RNA signatures affect start site selection. The TIS prediction model provides global estimates of TISs to discover neglected protein-coding genes across plant genomes. The prevalence of cis-regulatory signatures across plant species, humans, and viruses suggests their broad and critical roles in reprogramming the translational landscape.
Collapse
Affiliation(s)
- Ting-Ying Wu
- Institute of Plant and Microbial Biology, Academia Sinica, Taipei 11529, Taiwan;
| | - Ya-Ru Li
- Biotechnology Center in Southern Taiwan, Academia Sinica, Tainan 711, Taiwan
| | - Kai-Jyun Chang
- Biotechnology Center in Southern Taiwan, Academia Sinica, Tainan 711, Taiwan
- Institute of Tropical Plant Sciences, National Cheng Kung University, Tainan 701, Taiwan
| | - Jhen-Cheng Fang
- Biotechnology Center in Southern Taiwan, Academia Sinica, Tainan 711, Taiwan
| | - Daisuke Urano
- Temasek Life Sciences Laboratory, Singapore 117604, Singapore
- Department of Biological Sciences, National University of Singapore, Singapore 117558, Singapore
| | - Ming-Jung Liu
- Biotechnology Center in Southern Taiwan, Academia Sinica, Tainan 711, Taiwan;
- Institute of Tropical Plant Sciences, National Cheng Kung University, Tainan 701, Taiwan
- Agricultural Biotechnology Research Center, Academia Sinica, Taipei 115, Taiwan
| |
Collapse
|
4
|
Song YC, Das D, Zhang Y, Chen MX, Fernie AR, Zhu FY, Han J. Proteogenomics-based functional genome research: approaches, applications, and perspectives in plants. Trends Biotechnol 2023; 41:1532-1548. [PMID: 37365082 DOI: 10.1016/j.tibtech.2023.05.010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2023] [Revised: 05/17/2023] [Accepted: 05/30/2023] [Indexed: 06/28/2023]
Abstract
Proteogenomics (PG) integrates the proteome with the genome and transcriptome to refine gene models and annotation. Coupled with single-cell (SC) assays, PG effectively distinguishes heterogeneity among cell groups. Affiliating spatial information to PG reveals the high-resolution circuitry within SC atlases. Additionally, PG can investigate dynamic changes in protein-coding genes in plants across growth and development as well as stress and external stimulation, significantly contributing to the functional genome. Here we summarize existing PG research in plants and introduce the technical features of various methods. Combining PG with other omics, such as metabolomics and peptidomics, can offer even deeper insights into gene functions. We argue that the application of PG will represent an important font of foundational knowledge for plants.
Collapse
Affiliation(s)
- Yu-Chen Song
- State Key Laboratory of Tree Genetics and Breeding, Co-Innovation Center for Sustainable Forestry in Southern China, Key Laboratory of Tree Genetics and Biotechnology of Educational Department of China, Key Laboratory of State Forestry and Grassland Administration on Subtropical Forest Biodiversity Conservation, College of Life Sciences, Nanjing Forestry University, Nanjing 210037, China; College of Biology and Environment, Nanjing Forestry University, Nanjing 210037, China
| | - Debatosh Das
- College of Agriculture, Food and Natural Resources (CAFNR), Division of Plant Sciences and Technology, 52 Agricultural Building, University of Missouri-Columbia, MO 65201, USA
| | - Youjun Zhang
- Max-Planck-Institute of Molecular Plant Physiology, Am Mühlenberg 1, 14476 Potsdam-Golm, Germany; Center of Plant Systems Biology and Biotechnology, Plovdiv, Bulgaria
| | - Mo-Xian Chen
- State Key Laboratory of Tree Genetics and Breeding, Co-Innovation Center for Sustainable Forestry in Southern China, Key Laboratory of Tree Genetics and Biotechnology of Educational Department of China, Key Laboratory of State Forestry and Grassland Administration on Subtropical Forest Biodiversity Conservation, College of Life Sciences, Nanjing Forestry University, Nanjing 210037, China; College of Biology and Environment, Nanjing Forestry University, Nanjing 210037, China.
| | - Alisdair R Fernie
- Max-Planck-Institute of Molecular Plant Physiology, Am Mühlenberg 1, 14476 Potsdam-Golm, Germany; Center of Plant Systems Biology and Biotechnology, Plovdiv, Bulgaria.
| | - Fu-Yuan Zhu
- State Key Laboratory of Tree Genetics and Breeding, Co-Innovation Center for Sustainable Forestry in Southern China, Key Laboratory of Tree Genetics and Biotechnology of Educational Department of China, Key Laboratory of State Forestry and Grassland Administration on Subtropical Forest Biodiversity Conservation, College of Life Sciences, Nanjing Forestry University, Nanjing 210037, China; College of Biology and Environment, Nanjing Forestry University, Nanjing 210037, China.
| | - Jiangang Han
- State Key Laboratory of Tree Genetics and Breeding, Co-Innovation Center for Sustainable Forestry in Southern China, Key Laboratory of Tree Genetics and Biotechnology of Educational Department of China, Key Laboratory of State Forestry and Grassland Administration on Subtropical Forest Biodiversity Conservation, College of Life Sciences, Nanjing Forestry University, Nanjing 210037, China; College of Biology and Environment, Nanjing Forestry University, Nanjing 210037, China.
| |
Collapse
|
5
|
Fang JC, Liu MJ. Translation initiation at AUG and non-AUG triplets in plants. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2023; 335:111822. [PMID: 37574140 DOI: 10.1016/j.plantsci.2023.111822] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/15/2022] [Revised: 07/22/2023] [Accepted: 08/07/2023] [Indexed: 08/15/2023]
Abstract
In plants and other eukaryotes, precise selection of translation initiation site (TIS) on mRNAs shapes the proteome in response to cellular events or environmental cues. The canonical translation of mRNAs initiates at a 5' proximal AUG codon in a favorable context. However, the coding and non-coding regions of plant genomes contain numerous unannotated alternative AUG and non-AUG TISs. Determining how and why these unexpected and prevalent TISs are activated in plants has emerged as an exciting research area. In this review, we focus on the selection of plant TISs and highlight studies that revealed previously unannotated TISs used in vivo via comparative genomics and genome-wide profiling of ribosome positioning and protein N-terminal ends. The biological signatures of non-AUG TIS-initiated open reading frames (ORFs) in plants are also discussed. We describe what is understood about cis-regulatory RNA elements and trans-acting eukaryotic initiation factors (eIFs) in the site selection for translation initiation by featuring the findings in plants along with supporting findings in non-plant species. The prevalent, unannotated TISs provide a hidden reservoir of ORFs that likely help reshape plant proteomes in response to developmental or environmental cues. These findings underscore the importance of understanding the mechanistic basis of TIS selection to functionally annotate plant genomes, especially for crops with large genomes.
Collapse
Affiliation(s)
- Jhen-Cheng Fang
- Biotechnology Center in Southern Taiwan, Academia Sinica, Tainan 711, Taiwan
| | - Ming-Jung Liu
- Biotechnology Center in Southern Taiwan, Academia Sinica, Tainan 711, Taiwan; Agricultural Biotechnology Research Center, Academia Sinica, Taipei 115, Taiwan.
| |
Collapse
|
6
|
Vélez-Bermúdez IC, Chou SJ, Chen AP, Lin WD, Schmidt W. Protocol to measure ribosome density along mRNA transcripts of Arabidopsis thaliana tissues using Ribo-seq. STAR Protoc 2023; 4:102520. [PMID: 37597190 PMCID: PMC10469065 DOI: 10.1016/j.xpro.2023.102520] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2023] [Revised: 04/26/2023] [Accepted: 07/27/2023] [Indexed: 08/21/2023] Open
Abstract
Ribosome profiling (Ribo-seq) measures ribosome density along messenger RNA (mRNA) transcripts and is used to estimate the "translational fitness" of a given mRNA in response to environmental or developmental cues with high resolution. Here, we describe a protocol for Ribo-seq in plants adapted for the model plant Arabidopsis thaliana. We describe steps for lysis and nucleolytic digestion and ribosome footprinting. We then detail library construction, sequencing, and data analysis.
Collapse
Affiliation(s)
| | - Shu-Jen Chou
- Institute of Plant and Microbial Biology, Genomic Technology Core, Academia Sinica, Taipei 11529, Taiwan
| | - Ai-Ping Chen
- Institute of Plant and Microbial Biology, Genomic Technology Core, Academia Sinica, Taipei 11529, Taiwan
| | - Wen-Dar Lin
- Institute of Plant and Microbial Biology, Bioinformatics Core Lab, Academia Sinica, Taipei 11529, Taiwan
| | - Wolfgang Schmidt
- Institute of Plant and Microbial Biology, Academia Sinica, Taipei 11529, Taiwan.
| |
Collapse
|
7
|
Bogaert A, Fijalkowska D, Staes A, Van de Steene T, Demol H, Gevaert K. Limited evidence for protein products of non-coding transcripts in the HEK293T cellular cytosol. Mol Cell Proteomics 2022; 21:100264. [PMID: 35788065 PMCID: PMC9396073 DOI: 10.1016/j.mcpro.2022.100264] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2022] [Revised: 06/22/2022] [Accepted: 06/30/2022] [Indexed: 10/25/2022] Open
Abstract
Ribosome profiling has revealed translation outside of canonical coding sequences (CDSs) including translation of short upstream ORFs, long non-coding RNAs, overlapping ORFs, ORFs in UTRs or ORFs in alternative reading frames. Studies combining mass spectrometry, ribosome profiling and CRISPR-based screens showed that hundreds of ORFs derived from non-coding transcripts produce (micro)proteins, while other studies failed to find evidence for such types of non-canonical translation products. Here, we attempted to discover translation products from non-coding regions by strongly reducing the complexity of the sample prior to mass spectrometric analysis. We used an extended database as the search space and applied stringent filtering of the identified peptides to find evidence for novel translation events. We show that, theoretically our strategy facilitates the detection of translation events of transcripts from non-coding regions, but experimentally only find 19 peptides that might originate from such translation events. Finally, Virotrap based interactome analysis of two N-terminal proteoforms originating from non-coding regions finally showed the functional potential of these novel proteins.
Collapse
Affiliation(s)
- Annelies Bogaert
- VIB Center for Medical Biotechnology, VIB, Ghent, 9052, Belgium; Department of Biomolecular Medicine, Ghent University, Ghent, 9052, Belgium
| | - Daria Fijalkowska
- VIB Center for Medical Biotechnology, VIB, Ghent, 9052, Belgium; Department of Biomolecular Medicine, Ghent University, Ghent, 9052, Belgium
| | - An Staes
- VIB Center for Medical Biotechnology, VIB, Ghent, 9052, Belgium; Department of Biomolecular Medicine, Ghent University, Ghent, 9052, Belgium
| | - Tessa Van de Steene
- VIB Center for Medical Biotechnology, VIB, Ghent, 9052, Belgium; Department of Biomolecular Medicine, Ghent University, Ghent, 9052, Belgium
| | - Hans Demol
- VIB Center for Medical Biotechnology, VIB, Ghent, 9052, Belgium; Department of Biomolecular Medicine, Ghent University, Ghent, 9052, Belgium
| | - Kris Gevaert
- VIB Center for Medical Biotechnology, VIB, Ghent, 9052, Belgium; Department of Biomolecular Medicine, Ghent University, Ghent, 9052, Belgium.
| |
Collapse
|
8
|
Sahoo S, Singh D, Singh A, Pandit M, Vasu K, Som S, Pullagurla NJ, Laha D, Eswarappa SM. Identification and functional characterization of mRNAs that exhibit stop codon readthrough in Arabidopsis thaliana. J Biol Chem 2022; 298:102173. [PMID: 35752360 PMCID: PMC9293766 DOI: 10.1016/j.jbc.2022.102173] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2021] [Revised: 06/16/2022] [Accepted: 06/18/2022] [Indexed: 11/29/2022] Open
Abstract
Stop codon readthrough (SCR) is the process of continuation of translation beyond the stop codon, generating protein isoforms with C-terminal extensions. SCR has been observed in viruses, fungi, and multicellular organisms, including mammals. However, SCR is largely unexplored in plants. In this study, we have analyzed ribosome profiling datasets to identify mRNAs that exhibit SCR in Arabidopsis thaliana. Analyses of the ribosome density, ribosome coverage, and three-nucleotide periodicity of the ribosome profiling reads in the mRNA region downstream of the stop codon provided strong evidence for SCR in mRNAs of 144 genes. We show that SCR generated putative evolutionarily conserved nuclear localization signals, transmembrane helices, and intrinsically disordered regions in the C-terminal extensions of several of these proteins. Furthermore, gene ontology (GO) functional enrichment analysis revealed that these 144 genes belong to three major functional groups - translation, photosynthesis, and abiotic stress tolerance. Using a luminescence-based readthrough assay, we experimentally demonstrated SCR in representative mRNAs belonging to each of these functional classes. Finally, using microscopy, we show that the SCR product of one gene that contains a nuclear localization signal at the C-terminal extension, CURT1B, localizes to the nucleus as predicted. Based on these observations, we propose that SCR plays an important role in plant physiology by regulating protein localization and function.
Collapse
Affiliation(s)
- Sarthak Sahoo
- Undergraduate Program, Indian Institute of Science, Bengaluru, India; Department of Biochemistry, Indian Institute of Science, Bengaluru, India
| | - Divyoj Singh
- Undergraduate Program, Indian Institute of Science, Bengaluru, India
| | - Anumeha Singh
- Department of Biochemistry, Indian Institute of Science, Bengaluru, India
| | - Madhuparna Pandit
- Department of Biochemistry, Indian Institute of Science, Bengaluru, India
| | - Kirtana Vasu
- Department of Biochemistry, Indian Institute of Science, Bengaluru, India
| | - Saubhik Som
- Department of Biochemistry, Indian Institute of Science, Bengaluru, India
| | | | - Debabrata Laha
- Department of Biochemistry, Indian Institute of Science, Bengaluru, India
| | | |
Collapse
|
9
|
Sotta N, Chiba Y, Aoyama H, Takamatsu S, Suzuki T, Miwa K, Yamashita Y, Naito S, Fujiwara T. Translational Landscape of a C4 Plant, Sorghum bicolor, Under Normal and Sulfur-Deficient Conditions. PLANT & CELL PHYSIOLOGY 2022; 63:592-604. [PMID: 35166349 DOI: 10.1093/pcp/pcac023] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/16/2021] [Revised: 02/01/2022] [Accepted: 02/14/2022] [Indexed: 06/14/2023]
Abstract
Recent accumulation of genomic and transcriptomic information has facilitated genetic studies. Increasing evidence has demonstrated that translation is an important regulatory step, and the transcriptome does not necessarily reflect the profile of functional protein production. Deep sequencing of ribosome-protected mRNA fragments (ribosome profiling or Ribo-seq) has enabled genome-wide analysis of translation. Sorghum is a C4 cereal important not only as food but also as forage and a bioenergy resource. Its resistance to harsh environments has made it an agriculturally important research subject. Yet genome-wide translational profiles in sorghum are still missing. In this study, we took advantage of Ribo-seq and identified actively translated reading frames throughout the genome. We detected translation of 4,843 main open reading frames (ORFs) annotated in the sorghum reference genome version 3.1 and revealed a number of unannotated translational events. A comparison of the transcriptome and translatome between sorghums grown under normal and sulfur-deficient conditions revealed that gene expression is modulated independently at transcript and translation levels. Our study revealed the translational landscape of sorghum's response to sulfur and provides datasets that could serve as a fundamental resource to extend genetic research on sorghum, including studies on translational regulation.
Collapse
Affiliation(s)
- Naoyuki Sotta
- Graduate School of Agricultural and Life Sciences, The University of Tokyo, Tokyo, 113-8657 Japan
| | - Yukako Chiba
- Faculty of Science, Hokkaido University, Sapporo, 060-0810 Japan
- Graduate School of Life Science, Hokkaido University, Sapporo, 060-0810 Japan
| | - Haruka Aoyama
- Graduate School of Life Science, Hokkaido University, Sapporo, 060-0810 Japan
| | - Seidai Takamatsu
- Graduate School of Life Science, Hokkaido University, Sapporo, 060-0810 Japan
| | - Takamasa Suzuki
- Department of Biological Chemistry, College of Bioscience and Biotechnology, Chubu University, Kasugai, 487-8501 Japan
| | - Kyoko Miwa
- Graduate School of Environmental Science, Hokkaido University, Sapporo, 060-0810 Japan
| | - Yui Yamashita
- Graduate School of Agriculture, Hokkaido University, Sapporo, 060-8589 Japan
| | - Satoshi Naito
- Graduate School of Life Science, Hokkaido University, Sapporo, 060-0810 Japan
- Graduate School of Agriculture, Hokkaido University, Sapporo, 060-8589 Japan
| | - Toru Fujiwara
- Graduate School of Agricultural and Life Sciences, The University of Tokyo, Tokyo, 113-8657 Japan
| |
Collapse
|
10
|
Chiu CW, Li YR, Lin CY, Yeh HH, Liu MJ. Translation initiation landscape profiling reveals hidden open-reading frames required for the pathogenesis of tomato yellow leaf curl Thailand virus. THE PLANT CELL 2022; 34:1804-1821. [PMID: 35080617 PMCID: PMC9048955 DOI: 10.1093/plcell/koac019] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/10/2021] [Accepted: 01/06/2022] [Indexed: 05/12/2023]
Abstract
Plant viruses with densely packed genomes employ noncanonical translational strategies to increase the coding capacity for viral function. However, the diverse translational strategies used make it challenging to define the full set of viral genes. Here, using tomato yellow leaf curl Thailand virus (TYLCTHV, genus Begomovirus) as a model system, we identified genes beyond the annotated gene sets by experimentally profiling in vivo translation initiation sites (TISs). We found that unanticipated AUG TISs were prevalent and determined that their usage involves alternative transcriptional and/or translational start sites and is associated with flanking mRNA sequences. Specifically, two downstream in-frame TISs were identified in the viral gene AV2. These TISs were conserved in the begomovirus lineage and led to the translation of different protein isoforms localized to cytoplasmic puncta and at the cell periphery, respectively. In addition, we found translational evidence of an unexplored gene, BV2. BV2 is conserved among TYLCTHV isolates and localizes to the endoplasmic reticulum and plasmodesmata. Mutations of AV2 isoforms and BV2 significantly attenuated disease symptoms in tomato (Solanum lycopersicum). In conclusion, our study pinpointing in vivo TISs untangles the coding complexity of a plant viral genome and, more importantly, illustrates the biological significance of the hidden open-reading frames encoding viral factors for pathogenicity.
Collapse
Affiliation(s)
- Ching-Wen Chiu
- Biotechnology Center in Southern Taiwan, Academia Sinica, Tainan 711, Taiwan
| | - Ya-Ru Li
- Biotechnology Center in Southern Taiwan, Academia Sinica, Tainan 711, Taiwan
| | - Cheng-Yuan Lin
- Biotechnology Center in Southern Taiwan, Academia Sinica, Tainan 711, Taiwan
| | - Hsin-Hung Yeh
- Agricultural Biotechnology Research Center, Academia Sinica, Taipei 115, Taiwan
| | | |
Collapse
|
11
|
Willems P, Ndah E, Jonckheere V, Van Breusegem F, Van Damme P. To New Beginnings: Riboproteogenomics Discovery of N-Terminal Proteoforms in Arabidopsis Thaliana. FRONTIERS IN PLANT SCIENCE 2022; 12:778804. [PMID: 35069635 PMCID: PMC8770321 DOI: 10.3389/fpls.2021.778804] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/17/2021] [Accepted: 11/18/2021] [Indexed: 06/14/2023]
Abstract
Alternative translation initiation is a widespread event in biology that can shape multiple protein forms or proteoforms from a single gene. However, the respective contribution of alternative translation to protein complexity remains largely enigmatic. By complementary ribosome profiling and N-terminal proteomics (i.e., riboproteogenomics), we provide clear-cut evidence for ~90 N-terminal proteoform pairs shaped by (alternative) translation initiation in Arabidopsis thaliana. Next to several cases additionally confirmed by directed mutagenesis, identified alternative protein N-termini follow the enzymatic rules of co-translational N-terminal protein acetylation and initiator methionine removal. In contrast to other eukaryotic models, N-terminal acetylation in plants cannot generally be considered as a proxy of translation initiation because of its posttranslational occurrence on mature proteolytic neo-termini (N-termini) localized in the chloroplast stroma. Quantification of N-terminal acetylation revealed differing co- vs. posttranslational N-terminal acetylation patterns. Intriguingly, our data additionally hints to alternative translation initiation serving as a common mechanism to supply protein copies in multiple cellular compartments, as alternative translation sites are often in close proximity to cleavage sites of N-terminal transit sequences of nuclear-encoded chloroplastic and mitochondrial proteins. Overall, riboproteogenomics screening enables the identification of (differential localized) N-terminal proteoforms raised upon alternative translation.
Collapse
Affiliation(s)
- Patrick Willems
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
- Vlaams Instituut voor Biotechnologie (VIB)-Center for Plant Systems Biology, Ghent, Belgium
| | - Elvis Ndah
- integrative Riboproteogenomics, Interactomics and Proteomics Unit, Laboratory of Microbiology, Department of Biochemistry and Microbiology, Ghent University, Ghent, Belgium
| | - Veronique Jonckheere
- integrative Riboproteogenomics, Interactomics and Proteomics Unit, Laboratory of Microbiology, Department of Biochemistry and Microbiology, Ghent University, Ghent, Belgium
| | - Frank Van Breusegem
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
- Vlaams Instituut voor Biotechnologie (VIB)-Center for Plant Systems Biology, Ghent, Belgium
| | - Petra Van Damme
- integrative Riboproteogenomics, Interactomics and Proteomics Unit, Laboratory of Microbiology, Department of Biochemistry and Microbiology, Ghent University, Ghent, Belgium
| |
Collapse
|
12
|
Abstract
Modern genome-scale methods that identify new genes, such as proteogenomics and ribosome profiling, have revealed, to the surprise of many, that overlap in genes, open reading frames and even coding sequences is widespread and functionally integrated into prokaryotic, eukaryotic and viral genomes. In parallel, the constraints that overlapping regions place on genome sequences and their evolution can be harnessed in bioengineering to build more robust synthetic strains and constructs. With a focus on overlapping protein-coding and RNA-coding genes, this Review examines their discovery, topology and biogenesis in the context of their genome biology. We highlight exciting new uses for sequence overlap to control translation, compress synthetic genetic constructs, and protect against mutation.
Collapse
|
13
|
Heidorn-Czarna M, Maziak A, Janska H. Protein Processing in Plant Mitochondria Compared to Yeast and Mammals. FRONTIERS IN PLANT SCIENCE 2022; 13:824080. [PMID: 35185991 PMCID: PMC8847149 DOI: 10.3389/fpls.2022.824080] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/28/2021] [Accepted: 01/12/2022] [Indexed: 05/02/2023]
Abstract
Limited proteolysis, called protein processing, is an essential post-translational mechanism that controls protein localization, activity, and in consequence, function. This process is prevalent for mitochondrial proteins, mainly synthesized as precursor proteins with N-terminal sequences (presequences) that act as targeting signals and are removed upon import into the organelle. Mitochondria have a distinct and highly conserved proteolytic system that includes proteases with sole function in presequence processing and proteases, which show diverse mitochondrial functions with limited proteolysis as an additional one. In virtually all mitochondria, the primary processing of N-terminal signals is catalyzed by the well-characterized mitochondrial processing peptidase (MPP). Subsequently, a second proteolytic cleavage occurs, leading to more stabilized residues at the newly formed N-terminus. Lately, mitochondrial proteases, intermediate cleavage peptidase 55 (ICP55) and octapeptidyl protease 1 (OCT1), involved in proteolytic cleavage after MPP and their substrates have been described in the plant, yeast, and mammalian mitochondria. Mitochondrial proteins can also be processed by removing a peptide from their N- or C-terminus as a maturation step during insertion into the membrane or as a regulatory mechanism in maintaining their function. This type of limited proteolysis is characteristic for processing proteases, such as IMP and rhomboid proteases, or the general mitochondrial quality control proteases ATP23, m-AAA, i-AAA, and OMA1. Identification of processing protease substrates and defining their consensus cleavage motifs is now possible with the help of large-scale quantitative mass spectrometry-based N-terminomics, such as combined fractional diagonal chromatography (COFRADIC), charge-based fractional diagonal chromatography (ChaFRADIC), or terminal amine isotopic labeling of substrates (TAILS). This review summarizes the current knowledge on the characterization of mitochondrial processing peptidases and selected N-terminomics techniques used to uncover protease substrates in the plant, yeast, and mammalian mitochondria.
Collapse
|
14
|
Afonnikov DA, Sinitsyna OI, Golubeva TS, Shmakov NA, Kochetov AV. [Ribosomal profiling as a tool for studying translation in plants: main results, problems and future prospects]. Vavilovskii Zhurnal Genet Selektsii 2021; 25:251-259. [PMID: 34901721 PMCID: PMC8627869 DOI: 10.18699/vj21.028] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2020] [Revised: 12/08/2020] [Accepted: 12/08/2020] [Indexed: 11/19/2022] Open
Abstract
The expression of eukaryotic genes can be regulated at several stages, including the translation of mRNA. It is known that the structure of mRNA can affect both the efficiency of interaction with the translation apparatus in general and the choice of translation initiation sites. To study the translated fraction of the transcriptome, experimental methods of analysis were developed, the most informative of which is ribosomal profiling (RP, Ribo-seq). Originally developed for use in yeast systems, this method has been adapted for research in translation mechanisms in many plant species. This technology includes the isolation of the polysomal fraction and high-performance sequencing of a pool of mRNA fragments associated with ribosomes. Comparing the results of transcript coverage with reads obtained using the ribosome profiling with the transcriptional efficiency of genes allows the translation efficiency to be evaluated for each transcript. The exact positions of ribosomes determined on mRNA sequences allow determining the translation of open reading frames and switching between the translation of several reading frames - a phenomenon in which two or more overlapping frames are read from one mRNA and different proteins are synthesized. The advantage of this method is that it provides quantitative estimates of ribosome coverage of mRNA and can detect relatively rare translation events. Using this technology, it was possible to identify and classify plant genes by the type of regulation of their expression at the transcription, translation, or both levels. Features of the mRNA structure that affect translation levels have been revealed: the formation of G2 quadruplexes and the presence of specific motifs in the 5'-UTR region, GC content, the presence of alternative translation starts, and the influence of uORFs on the translation of downstream mORFs. In this review, we briefly reviewed the RP methodology and the prospects for its application to study the structural and functional organization and regulation of plant gene expression.
Collapse
Affiliation(s)
- D A Afonnikov
- Institute of Cytology and Genetics of the Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia Novosibirsk State University, Novosibirsk, Russia
| | - O I Sinitsyna
- Institute of Cytology and Genetics of the Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia Novosibirsk State University, Novosibirsk, Russia
| | - T S Golubeva
- Institute of Cytology and Genetics of the Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia Novosibirsk State University, Novosibirsk, Russia
| | - N A Shmakov
- Institute of Cytology and Genetics of the Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia Novosibirsk State University, Novosibirsk, Russia
| | - A V Kochetov
- Institute of Cytology and Genetics of the Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia Novosibirsk State University, Novosibirsk, Russia
| |
Collapse
|
15
|
van Wijk KJ, Leppert T, Sun Q, Boguraev SS, Sun Z, Mendoza L, Deutsch EW. The Arabidopsis PeptideAtlas: Harnessing worldwide proteomics data to create a comprehensive community proteomics resource. THE PLANT CELL 2021; 33:3421-3453. [PMID: 34411258 PMCID: PMC8566204 DOI: 10.1093/plcell/koab211] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/03/2021] [Accepted: 08/13/2021] [Indexed: 05/02/2023]
Abstract
We developed a resource, the Arabidopsis PeptideAtlas (www.peptideatlas.org/builds/arabidopsis/), to solve central questions about the Arabidopsis thaliana proteome, such as the significance of protein splice forms and post-translational modifications (PTMs), or simply to obtain reliable information about specific proteins. PeptideAtlas is based on published mass spectrometry (MS) data collected through ProteomeXchange and reanalyzed through a uniform processing and metadata annotation pipeline. All matched MS-derived peptide data are linked to spectral, technical, and biological metadata. Nearly 40 million out of ∼143 million MS/MS (tandem MS) spectra were matched to the reference genome Araport11, identifying ∼0.5 million unique peptides and 17,858 uniquely identified proteins (only isoform per gene) at the highest confidence level (false discovery rate 0.0004; 2 non-nested peptides ≥9 amino acid each), assigned canonical proteins, and 3,543 lower-confidence proteins. Physicochemical protein properties were evaluated for targeted identification of unobserved proteins. Additional proteins and isoforms currently not in Araport11 were identified that were generated from pseudogenes, alternative start, stops, and/or splice variants, and small Open Reading Frames; these features should be considered when updating the Arabidopsis genome. Phosphorylation can be inspected through a sophisticated PTM viewer. PeptideAtlas is integrated with community resources including TAIR, tracks in JBrowse, PPDB, and UniProtKB. Subsequent PeptideAtlas builds will incorporate millions more MS/MS data.
Collapse
Affiliation(s)
- Klaas J van Wijk
- Section of Plant Biology, School of Integrative Plant Sciences (SIPS), Cornell University, Ithaca, New York 14853, USA
- Authors for correspondence: (K.J.V.W.), (E.W.D.)
| | - Tami Leppert
- Institute for Systems Biology (ISB), Seattle, Washington 98109, USA
| | - Qi Sun
- Computational Biology Service Unit, Cornell University, Ithaca, New York 14853, USA
| | - Sascha S Boguraev
- Section of Plant Biology, School of Integrative Plant Sciences (SIPS), Cornell University, Ithaca, New York 14853, USA
| | - Zhi Sun
- Institute for Systems Biology (ISB), Seattle, Washington 98109, USA
| | - Luis Mendoza
- Institute for Systems Biology (ISB), Seattle, Washington 98109, USA
| | - Eric W Deutsch
- Institute for Systems Biology (ISB), Seattle, Washington 98109, USA
- Authors for correspondence: (K.J.V.W.), (E.W.D.)
| |
Collapse
|
16
|
Van Damme P. Charting the N-Terminal Acetylome: A Comprehensive Map of Human NatA Substrates. Int J Mol Sci 2021; 22:ijms221910692. [PMID: 34639033 PMCID: PMC8509067 DOI: 10.3390/ijms221910692] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2021] [Revised: 09/10/2021] [Accepted: 09/29/2021] [Indexed: 11/29/2022] Open
Abstract
N-terminal acetylation (Nt-acetylation) catalyzed by conserved N-terminal acetyltransferases or NATs embodies a modification with one of the highest stoichiometries reported for eukaryotic protein modifications to date. Comprising the catalytic N-alpha acetyltransferase (NAA) subunit NAA10 plus the ribosome anchoring regulatory subunit NAA15, NatA represents the major acetyltransferase complex with up to 50% of all mammalian proteins representing potential substrates. Largely in consequence of the essential nature of NatA and its high enzymatic activity, its experimentally confirmed mammalian substrate repertoire remained poorly charted. In this study, human NatA knockdown conditions achieving near complete depletion of NAA10 and NAA15 expression resulted in lowered Nt-acetylation of over 25% out of all putative NatA targets identified, representing an up to 10-fold increase in the reported number of substrate N-termini affected upon human NatA perturbation. Besides pointing to less efficient NatA substrates being prime targets, several putative NatE substrates were shown to be affected upon human NatA knockdown. Intriguingly, next to a lowered expression of ribosomal proteins and proteins constituting the eukaryotic 48S preinitiation complex, steady-state levels of protein N-termini additionally point to NatA Nt-acetylation deficiency directly impacting protein stability of knockdown affected targets.
Collapse
Affiliation(s)
- Petra Van Damme
- iRIP Unit, Laboratory of Microbiology, Department of Biochemistry and Microbiology, Ghent University, K. L. Ledeganckstraat 35, 9000 Ghent, Belgium
| |
Collapse
|
17
|
He C, Guo J, Tian W, Wong CCL. Proteogenomics Integrating Novel Junction Peptide Identification Strategy Discovers Three Novel Protein Isoforms of Human NHSL1 and EEF1B2. J Proteome Res 2021; 20:5294-5303. [PMID: 34420305 DOI: 10.1021/acs.jproteome.1c00373] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
In eukaryotes, alternative pre-mRNA splicing allows a single gene to encode different protein isoforms that function in many biological processes, and they are used as biomarkers or therapeutic targets for diseases. Although protein isoforms in the human genome are well annotated, we speculate that some low-abundance protein isoforms may still be under-annotated because most genes have a primary coding product and alternative protein isoforms tend to be under-expressed. A peptide coencoded by a novel exon and an annotated exon separated by an intron is known as a novel junction peptide. In the absence of known transcripts and homologous proteins, traditional whole-genome six-frame translation-based proteogenomics cannot identify novel junction peptides, and it cannot capture novel alternative splice sites. In this article, we first propose a strategy and tool for identifying novel junction peptides, called CJunction, which we then integrate into a proteogenomics process specifically designed for novel protein isoform discovery and apply to the analysis of a deep-coverage HeLa mass spectrometry data set with identifier PXD004452 in ProteomeXchange. We succeeded in identifying and validating three novel protein isoforms of two functionally important genes, NHSL1 (causative gene of Nance-Horan syndrome) and EEF1B2 (translation elongation factor), which validate our hypothesis. These novel protein isoforms have significant sequence differences from the annotated gene-coding products introduced by the novel N-terminal, suggesting that they may play importantly different functions.
Collapse
Affiliation(s)
- Cuitong He
- Peking-Tsinghua Centre for Life Sciences, Academy for Advanced Interdisciplinary Studies, Peking University, 100871 Beijing, China.,Center for Precision Medicine Multi-Omics Research, Peking University Health Science Center, 100191 Beijing, China
| | - Jiangtao Guo
- Center for Precision Medicine Multi-Omics Research, Peking University Health Science Center, 100191 Beijing, China
| | - Wenmin Tian
- Center for Precision Medicine Multi-Omics Research, Peking University Health Science Center, 100191 Beijing, China.,School of Basic Medical Sciences, Peking University Health Science Center, 100191 Beijing, China
| | - Catherine C L Wong
- Peking-Tsinghua Centre for Life Sciences, Academy for Advanced Interdisciplinary Studies, Peking University, 100871 Beijing, China.,Center for Precision Medicine Multi-Omics Research, Peking University Health Science Center, 100191 Beijing, China.,School of Basic Medical Sciences, Peking University Health Science Center, 100191 Beijing, China.,Peking University First Hospital, 100034 Beijing, China.,Advanced Innovation Center for Human Brain Protection, Capital Medical University, 100069 Beijing, China
| |
Collapse
|
18
|
Lost and Found: Re-searching and Re-scoring Proteomics Data Aids Genome Annotation and Improves Proteome Coverage. mSystems 2020; 5:5/5/e00833-20. [PMID: 33109751 PMCID: PMC7593589 DOI: 10.1128/msystems.00833-20] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023] Open
Abstract
Delineation of open reading frames (ORFs) causes persistent inconsistencies in prokaryote genome annotation. We demonstrate that by advanced (re)analysis of omics data, a higher proteome coverage and sensitive detection of unannotated ORFs can be achieved, which can be exploited for conditional bacterial genome (re)annotation, which is especially relevant in view of annotating the wealth of sequenced prokaryotic genomes obtained in recent years. Prokaryotic genome annotation is heavily dependent on automated gene annotation pipelines that are prone to propagate errors and underestimate genome complexity. We describe an optimized proteogenomic workflow that uses ribosome profiling (ribo-seq) and proteomic data for Salmonella enterica serovar Typhimurium to identify unannotated proteins or alternative protein forms. This data analysis encompasses the searching of cofragmenting peptides and postprocessing with extended peptide-to-spectrum quality features, including comparison to predicted fragment ion intensities. When this strategy is applied, an enhanced proteome depth is achieved, as well as greater confidence for unannotated peptide hits. We demonstrate the general applicability of our pipeline by reanalyzing public Deinococcus radiodurans data sets. Taken together, our results show that systematic reanalysis using available prokaryotic (proteome) data sets holds great promise to assist in experimentally based genome annotation. IMPORTANCE Delineation of open reading frames (ORFs) causes persistent inconsistencies in prokaryote genome annotation. We demonstrate that by advanced (re)analysis of omics data, a higher proteome coverage and sensitive detection of unannotated ORFs can be achieved, which can be exploited for conditional bacterial genome (re)annotation, which is especially relevant in view of annotating the wealth of sequenced prokaryotic genomes obtained in recent years.
Collapse
|
19
|
Li YR, Liu MJ. Prevalence of alternative AUG and non-AUG translation initiators and their regulatory effects across plants. Genome Res 2020; 30:1418-1433. [PMID: 32973042 PMCID: PMC7605272 DOI: 10.1101/gr.261834.120] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2020] [Accepted: 08/19/2020] [Indexed: 12/11/2022]
Abstract
Translation initiation is a key step determining protein synthesis. Studies have uncovered a number of alternative translation initiation sites (TISs) in mammalian mRNAs and showed their roles in reshaping the proteome. However, the extent to which alternative TISs affect gene expression across plants remains largely unclear. Here, by profiling initiating ribosome positions, we globally identified in vivo TISs in tomato and Arabidopsis and found thousands of genes with more than one TIS. Of the identified TISs, >19% and >20% were located at unannotated AUG and non-AUG sites, respectively. CUG and ACG were the most frequently observed codons at non-AUG TISs, a phenomenon also found in mammals. In addition, although alternative TISs were usually found in both orthologous genes, the TIS sequences were not conserved, suggesting the conservation of alternative initiation mechanisms but flexibility in using TISs. Unlike upstream AUG TISs, the presence of upstream non-AUG TISs was not correlated with the translational repression of main open reading frames, a pattern observed across plants. Also, the generation of proteins with diverse N-terminal regions through the use of alternative TISs contributes to differential subcellular localization, as mutating alternative TISs resulted in the loss of organelle localization. Our findings uncovered the hidden coding potential of plant genomes and, importantly, the constraint and flexibility of translational initiation mechanisms in the regulation of gene expression across plant species.
Collapse
Affiliation(s)
- Ya-Ru Li
- Biotechnology Center in Southern Taiwan, Academia Sinica, Tainan 741, Taiwan
| | - Ming-Jung Liu
- Biotechnology Center in Southern Taiwan, Academia Sinica, Tainan 741, Taiwan.,Agricultural Biotechnology Research Center, Academia Sinica, Taipei 115, Taiwan
| |
Collapse
|
20
|
Kage U, Powell JJ, Gardiner DM, Kazan K. Ribosome profiling in plants: what is not lost in translation? JOURNAL OF EXPERIMENTAL BOTANY 2020; 71:5323-5332. [PMID: 32459844 DOI: 10.1093/jxb/eraa227] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/10/2020] [Accepted: 05/05/2020] [Indexed: 05/03/2023]
Abstract
Translation is a highly dynamic cellular process whereby genetic information residing in an mRNA molecule is converted into a protein that in turn executes specific functions. However, pre-synthesized mRNA levels do not always correlate with corresponding protein levels, suggesting that translational control plays an essential role in gene regulation. A better understanding of how gene expression is regulated during translation will enable the discovery of new genes and mechanisms that control important traits in plants. Therefore, in recent years, several methods have been developed to analyse the translatome; that is, all mRNAs being actively translated at a given time, tissue, and/or developmental stage. Ribosome profiling or ribo-seq is one such technology revolutionizing our ability to analyse the translatome and in turn understand translational control of gene expression. Ribo-seq involves isolating mRNA-ribosome complexes, treating them with a RNase, and then identifying ribosome-protected mRNA regions by deep sequencing. Here, we briefly review recent ribosome profiling studies that revealed new insights into plant biology. Manipulation of novel genes identified using ribosome profiling could prove useful for increasing yield through improved biotic and abiotic stress tolerance.
Collapse
Affiliation(s)
- Udaykumar Kage
- Commonwealth Scientific and Industrial Research Organisation, Agriculture and Food, St Lucia, QLD, Australia
| | - Jonathan J Powell
- Commonwealth Scientific and Industrial Research Organisation, Agriculture and Food, St Lucia, QLD, Australia
| | - Donald M Gardiner
- Commonwealth Scientific and Industrial Research Organisation, Agriculture and Food, St Lucia, QLD, Australia
| | - Kemal Kazan
- Commonwealth Scientific and Industrial Research Organisation, Agriculture and Food, St Lucia, QLD, Australia
| |
Collapse
|
21
|
Gabriels R, Martens L, Degroeve S. Updated MS²PIP web server delivers fast and accurate MS² peak intensity prediction for multiple fragmentation methods, instruments and labeling techniques. Nucleic Acids Res 2020; 47:W295-W299. [PMID: 31028400 PMCID: PMC6602496 DOI: 10.1093/nar/gkz299] [Citation(s) in RCA: 56] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2019] [Revised: 04/14/2019] [Accepted: 04/24/2019] [Indexed: 12/13/2022] Open
Abstract
MS²PIP is a data-driven tool that accurately predicts peak intensities for a given peptide's fragmentation mass spectrum. Since the release of the MS²PIP web server in 2015, we have brought significant updates to both the tool and the web server. In addition to the original models for CID and HCD fragmentation, we have added specialized models for the TripleTOF 5600+ mass spectrometer, for TMT-labeled peptides, for iTRAQ-labeled peptides, and for iTRAQ-labeled phosphopeptides. Because the fragmentation pattern is heavily altered in each of these cases, these additional models greatly improve the prediction accuracy for their corresponding data types. We have also substantially reduced the computational resources required to run MS²PIP, and have completely rebuilt the web server, which now allows predictions of up to 100 000 peptide sequences in a single request. The MS²PIP web server is freely available at https://iomics.ugent.be/ms2pip/.
Collapse
Affiliation(s)
- Ralf Gabriels
- VIB-UGent Center for Medical Biotechnology, VIB, A. Baertsoenkaai 3, B9000 Ghent, Belgium.,Department of Biomolecular Medicine, Ghent University, Ghent, Belgium
| | - Lennart Martens
- VIB-UGent Center for Medical Biotechnology, VIB, A. Baertsoenkaai 3, B9000 Ghent, Belgium.,Department of Biomolecular Medicine, Ghent University, Ghent, Belgium
| | - Sven Degroeve
- VIB-UGent Center for Medical Biotechnology, VIB, A. Baertsoenkaai 3, B9000 Ghent, Belgium.,Department of Biomolecular Medicine, Ghent University, Ghent, Belgium
| |
Collapse
|
22
|
Niedermaier S, Huesgen PF. Positional proteomics for identification of secreted proteoforms released by site-specific processing of membrane proteins. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2019; 1867:140138. [DOI: 10.1016/j.bbapap.2018.09.004] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/09/2018] [Revised: 08/31/2018] [Accepted: 09/13/2018] [Indexed: 02/06/2023]
|
23
|
Weng SSH, Demir F, Ergin EK, Dirnberger S, Uzozie A, Tuscher D, Nierves L, Tsui J, Huesgen PF, Lange PF. Sensitive Determination of Proteolytic Proteoforms in Limited Microscale Proteome Samples. Mol Cell Proteomics 2019; 18:2335-2347. [PMID: 31471496 PMCID: PMC6823850 DOI: 10.1074/mcp.tir119.001560] [Citation(s) in RCA: 54] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2019] [Revised: 08/09/2019] [Indexed: 12/15/2022] Open
Abstract
Protein N termini unambiguously identify truncated, alternatively translated or modified proteoforms with distinct functions and reveal perturbations in disease. Selective enrichment of N-terminal peptides is necessary to achieve proteome-wide coverage for unbiased identification of site-specific regulatory proteolytic processing and protease substrates. However, many proteolytic processes are strictly confined in time and space and therefore can only be analyzed in minute samples that provide insufficient starting material for current enrichment protocols. Here we present High-efficiency Undecanal-based N Termini EnRichment (HUNTER), a robust, sensitive and scalable method for the analysis of previously inaccessible microscale samples. HUNTER achieved identification of >1000 N termini from as little as 2 μg raw HeLa cell lysate. Broad applicability is demonstrated by the first N-terminome analysis of sorted human primary immune cells and enriched mitochondrial fractions from pediatric cancer patients, as well as protease substrate identification from individual Arabidopsis thaliana wild type and Vacuolar Processing Enzyme-deficient mutant seedlings. We further implemented the workflow on a liquid handling system and demonstrate the feasibility of clinical degradomics by automated processing of liquid biopsies from pediatric cancer patients.
Collapse
Affiliation(s)
- Samuel S H Weng
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, Canada; Michael Cuccione Childhood Cancer Research Program, BC Children's Hospital, Vancouver, Canada
| | - Fatih Demir
- Central Institute for Engineering, Electronics and Analytics, ZEA-3, Forschungszentrum Jülich, Germany
| | - Enes K Ergin
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, Canada; Michael Cuccione Childhood Cancer Research Program, BC Children's Hospital, Vancouver, Canada
| | - Sabrina Dirnberger
- Central Institute for Engineering, Electronics and Analytics, ZEA-3, Forschungszentrum Jülich, Germany
| | - Anuli Uzozie
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, Canada; Michael Cuccione Childhood Cancer Research Program, BC Children's Hospital, Vancouver, Canada
| | - Domenic Tuscher
- Central Institute for Engineering, Electronics and Analytics, ZEA-3, Forschungszentrum Jülich, Germany
| | - Lorenz Nierves
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, Canada; Michael Cuccione Childhood Cancer Research Program, BC Children's Hospital, Vancouver, Canada
| | - Janice Tsui
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, Canada; Michael Cuccione Childhood Cancer Research Program, BC Children's Hospital, Vancouver, Canada
| | - Pitter F Huesgen
- Central Institute for Engineering, Electronics and Analytics, ZEA-3, Forschungszentrum Jülich, Germany; Cologne Excellence Cluster on Cellular Stress Responses in Aging Associated Diseases, Medical Faculty and University Hospital, University of Cologne, Cologne, Germany.
| | - Philipp F Lange
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, Canada; Michael Cuccione Childhood Cancer Research Program, BC Children's Hospital, Vancouver, Canada.
| |
Collapse
|
24
|
Sun P, Li G. CircCode: A Powerful Tool for Identifying circRNA Coding Ability. Front Genet 2019; 10:981. [PMID: 31649739 PMCID: PMC6795751 DOI: 10.3389/fgene.2019.00981] [Citation(s) in RCA: 37] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2019] [Accepted: 09/13/2019] [Indexed: 01/25/2023] Open
Abstract
Circular RNAs (circRNAs), which play vital roles in many regulatory pathways, are widespread in many species. Although many circRNAs have been discovered in plants and animals, the functions of these RNAs have not been fully investigated. In addition to the function of circRNAs as microRNA (miRNA) decoys, the translation potential of circRNAs is important for the study of their functions; yet, few tools are available to identify their translation potential. With the development of high-throughput sequencing technology and the emergence of ribosome profiling technology, it is possible to identify the coding ability of circRNAs with high sensitivity. To evaluate the coding ability of circRNAs, we first developed the CircCode tool and then used CircCode to investigate the translation potential of circRNAs from humans and Arabidopsis thaliana. Based on the ribosome profile databases downloaded from NCBI, we found 3,610 and 1,569 translated circRNAs in humans and A. thaliana, respectively. Finally, we tested the performance of CircCode and found a low false discovery rate and high sensitivity for identifying circRNA coding ability. CircCode, a Python 3-based framework for identifying the coding ability of circRNAs, is also a simple and powerful command line-based tool. To investigate the translation potential of circRNAs, the user can simply fill in the given configuration file and run the Python 3 scripts. The tool is freely available at https://github.com/PSSUN/CircCode.
Collapse
Affiliation(s)
- Peisen Sun
- Key Laboratory of Ministry of Education for Medicinal Plant Resource and Natural Pharmaceutical Chemistry, Shaanxi Normal University, Xi’an, China
- College of Life Sciences, Shaanxi Normal University, Xi’an, China
| | - Guanglin Li
- Key Laboratory of Ministry of Education for Medicinal Plant Resource and Natural Pharmaceutical Chemistry, Shaanxi Normal University, Xi’an, China
- College of Life Sciences, Shaanxi Normal University, Xi’an, China
| |
Collapse
|
25
|
Korandla DR, Wozniak JM, Campeau A, Gonzalez DJ, Wright ES. AssessORF: combining evolutionary conservation and proteomics to assess prokaryotic gene predictions. Bioinformatics 2019; 36:1022-1029. [PMID: 31532487 PMCID: PMC7998711 DOI: 10.1093/bioinformatics/btz714] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2019] [Revised: 09/05/2019] [Accepted: 09/13/2019] [Indexed: 01/31/2023] Open
Abstract
MOTIVATION A core task of genomics is to identify the boundaries of protein coding genes, which may cover over 90% of a prokaryote's genome. Several programs are available for gene finding, yet it is currently unclear how well these programs perform and whether any offers superior accuracy. This is in part because there is no universal benchmark for gene finding and, therefore, most developers select their own benchmarking strategy. RESULTS Here, we introduce AssessORF, a new approach for benchmarking prokaryotic gene predictions based on evidence from proteomics data and the evolutionary conservation of start and stop codons. We applied AssessORF to compare gene predictions offered by GenBank, GeneMarkS-2, Glimmer and Prodigal on genomes spanning the prokaryotic tree of life. Gene predictions were 88-95% in agreement with the available evidence, with Glimmer performing the worst but no clear winner. All programs were biased towards selecting start codons that were upstream of the actual start. Given these findings, there remains considerable room for improvement, especially in the detection of correct start sites. AVAILABILITY AND IMPLEMENTATION AssessORF is available as an R package via the Bioconductor package repository. SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
Collapse
Affiliation(s)
- Deepank R Korandla
- Department of Biological Sciences, USA,Computational Biology Department, Carnegie Mellon University, Pittsburgh, PA 15213, USA,Department of Biomedical Informatics, University of Pittsburgh School of Medicine, Pittsburgh, PA 15219, USA
| | - Jacob M Wozniak
- Department of Pharmacology, University of California San Diego, La Jolla, CA 92093, USA,Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA 92093, USA
| | - Anaamika Campeau
- Department of Pharmacology, University of California San Diego, La Jolla, CA 92093, USA,Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA 92093, USA
| | - David J Gonzalez
- Department of Pharmacology, University of California San Diego, La Jolla, CA 92093, USA,Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA 92093, USA
| | | |
Collapse
|
26
|
Hander T, Fernández-Fernández ÁD, Kumpf RP, Willems P, Schatowitz H, Rombaut D, Staes A, Nolf J, Pottie R, Yao P, Gonçalves A, Pavie B, Boller T, Gevaert K, Van Breusegem F, Bartels S, Stael S. Damage on plants activates Ca 2+-dependent metacaspases for release of immunomodulatory peptides. Science 2019; 363:363/6433/eaar7486. [PMID: 30898901 DOI: 10.1126/science.aar7486] [Citation(s) in RCA: 144] [Impact Index Per Article: 28.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2017] [Revised: 12/06/2018] [Accepted: 02/13/2019] [Indexed: 12/14/2022]
Abstract
Physical damage to cells leads to the release of immunomodulatory peptides to elicit a wound defense response in the surrounding tissue. In Arabidopsis thaliana, the plant elicitor peptide 1 (Pep1) is processed from its protein precursor, PRECURSOR OF PEP1 (PROPEP1). We demonstrate that upon damage, both at the tissue and single-cell levels, the cysteine protease METACASPASE4 (MC4) is instantly and spatiotemporally activated by binding high levels of Ca2+ and is necessary and sufficient for Pep1 maturation. Cytosol-localized PROPEP1 and MC4 react only after loss of plasma membrane integrity and prolonged extracellular Ca2+ entry. Our results reveal that a robust mechanism consisting of conserved molecular components links the intracellular and Ca2+-dependent activation of a specific cysteine protease with the maturation of damage-induced wound defense signals.
Collapse
Affiliation(s)
- Tim Hander
- Zürich-Basel Plant Science Center, Department of Environmental Sciences, Botany, University of Basel, 4056 Basel, Switzerland
| | - Álvaro D Fernández-Fernández
- Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium.,VIB-UGent Center for Plant Systems Biology, 9052 Ghent, Belgium
| | - Robert P Kumpf
- Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium.,VIB-UGent Center for Plant Systems Biology, 9052 Ghent, Belgium
| | - Patrick Willems
- Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium.,VIB-UGent Center for Plant Systems Biology, 9052 Ghent, Belgium.,Department of Biomolecular Medicine, Ghent University, 9000 Ghent, Belgium.,VIB-UGent Center for Medical Biotechnology, 9000 Ghent, Belgium
| | - Hendrik Schatowitz
- Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium.,VIB-UGent Center for Plant Systems Biology, 9052 Ghent, Belgium
| | - Debbie Rombaut
- Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium.,VIB-UGent Center for Plant Systems Biology, 9052 Ghent, Belgium
| | - An Staes
- Department of Biomolecular Medicine, Ghent University, 9000 Ghent, Belgium.,VIB-UGent Center for Medical Biotechnology, 9000 Ghent, Belgium
| | - Jonah Nolf
- Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium.,VIB-UGent Center for Plant Systems Biology, 9052 Ghent, Belgium
| | - Robin Pottie
- Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium.,VIB-UGent Center for Plant Systems Biology, 9052 Ghent, Belgium
| | - Panfeng Yao
- Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium.,VIB-UGent Center for Plant Systems Biology, 9052 Ghent, Belgium
| | - Amanda Gonçalves
- VIB BioImaging Core Gent, VIB-UGent Center for Inflammation Research (IRC), 9052 Ghent, Belgium
| | - Benjamin Pavie
- VIB BioImaging Core Gent, VIB-UGent Center for Inflammation Research (IRC), 9052 Ghent, Belgium
| | - Thomas Boller
- Zürich-Basel Plant Science Center, Department of Environmental Sciences, Botany, University of Basel, 4056 Basel, Switzerland
| | - Kris Gevaert
- Department of Biomolecular Medicine, Ghent University, 9000 Ghent, Belgium.,VIB-UGent Center for Medical Biotechnology, 9000 Ghent, Belgium
| | - Frank Van Breusegem
- Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium.,VIB-UGent Center for Plant Systems Biology, 9052 Ghent, Belgium
| | - Sebastian Bartels
- Zürich-Basel Plant Science Center, Department of Environmental Sciences, Botany, University of Basel, 4056 Basel, Switzerland.,Department of Medicine II, University Hospital Freiburg-Faculty of Medicine, University of Freiburg, 79106 Freiburg, Germany
| | - Simon Stael
- Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium. .,VIB-UGent Center for Plant Systems Biology, 9052 Ghent, Belgium.,Department of Biomolecular Medicine, Ghent University, 9000 Ghent, Belgium.,VIB-UGent Center for Medical Biotechnology, 9000 Ghent, Belgium
| |
Collapse
|
27
|
Xu Z, Hu L, Shi B, Geng S, Xu L, Wang D, Lu ZJ. Ribosome elongating footprints denoised by wavelet transform comprehensively characterize dynamic cellular translation events. Nucleic Acids Res 2019; 46:e109. [PMID: 29945224 PMCID: PMC6182183 DOI: 10.1093/nar/gky533] [Citation(s) in RCA: 33] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2018] [Accepted: 05/31/2018] [Indexed: 02/06/2023] Open
Abstract
Translation is dynamically regulated during cell development and stress response. In order to detect actively translated open reading frames (ORFs) and dynamic cellular translation events, we have developed a computational method, RiboWave, to process ribosome profiling data. RiboWave utilizes wavelet transform to denoise the original signal by extracting 3-nt periodicity of ribosomes and precisely locate their footprint denoted as Periodic Footprint P-site (PF P-site). Such high-resolution footprint is found to capture the full track of actively elongating ribosomes, from which translational landscape can be explicitly characterized. We compare RiboWave with several published methods, like RiboTaper, ORFscore and RibORF, and found that RiboWave outperforms them in both accuracy and usage when defining actively translated ORFs. Moreover, we show that PF P-site derived by RiboWave shows superior performance in characterizing the dynamics and complexity of cellular translatome by accurately estimating the abundance of protein levels, assessing differential translation and identifying dynamic translation frameshift.
Collapse
Affiliation(s)
- Zhiyu Xu
- MOE Key Laboratory of Bioinformatics, Center for Synthetic and Systems Biology, School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Long Hu
- MOE Key Laboratory of Bioinformatics, Center for Synthetic and Systems Biology, School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Binbin Shi
- MOE Key Laboratory of Bioinformatics, Center for Synthetic and Systems Biology, School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - SiSi Geng
- MOE Key Laboratory of Bioinformatics, Center for Synthetic and Systems Biology, School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Longchen Xu
- MOE Key Laboratory of Bioinformatics, Center for Synthetic and Systems Biology, School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Dong Wang
- MOE Key Laboratory of Bioinformatics, Center for Synthetic and Systems Biology, School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Zhi J Lu
- MOE Key Laboratory of Bioinformatics, Center for Synthetic and Systems Biology, School of Life Sciences, Tsinghua University, Beijing 100084, China
| |
Collapse
|
28
|
Verbruggen S, Ndah E, Van Criekinge W, Gessulat S, Kuster B, Wilhelm M, Van Damme P, Menschaert G. PROTEOFORMER 2.0: Further Developments in the Ribosome Profiling-assisted Proteogenomic Hunt for New Proteoforms. Mol Cell Proteomics 2019; 18:S126-S140. [PMID: 31040227 PMCID: PMC6692777 DOI: 10.1074/mcp.ra118.001218] [Citation(s) in RCA: 32] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2018] [Revised: 04/30/2019] [Indexed: 12/20/2022] Open
Abstract
PROTEOFORMER is a pipeline that enables the automated processing of data derived from ribosome profiling (RIBO-seq, i.e. the sequencing of ribosome-protected mRNA fragments). As such, genome-wide ribosome occupancies lead to the delineation of data-specific translation product candidates and these can improve the mass spectrometry-based identification. Since its first publication, different upgrades, new features and extensions have been added to the PROTEOFORMER pipeline. Some of the most important upgrades include P-site offset calculation during mapping, comprehensive data pre-exploration, the introduction of two alternative proteoform calling strategies and extended pipeline output features. These novelties are illustrated by analyzing ribosome profiling data of human HCT116 and Jurkat data. The different proteoform calling strategies are used alongside one another and in the end combined together with reference sequences from UniProt. Matching mass spectrometry data are searched against this extended search space with MaxQuant. Overall, besides annotated proteoforms, this pipeline leads to the identification and validation of different categories of new proteoforms, including translation products of up- and downstream open reading frames, 5' and 3' extended and truncated proteoforms, single amino acid variants, splice variants and translation products of so-called noncoding regions. Further, proof-of-concept is reported for the improvement of spectrum matching by including Prosit, a deep neural network strategy that adds extra fragmentation spectrum intensity features to the analysis. In the light of ribosome profiling-driven proteogenomics, it is shown that this allows validating the spectrum matches of newly identified proteoforms with elevated stringency. These updates and novel conclusions provide new insights and lessons for the ribosome profiling-based proteogenomic research field. More practical information on the pipeline, raw code, the user manual (README) and explanations on the different modes of availability can be found at the GitHub repository of PROTEOFORMER: https://github.com/Biobix/proteoformer.
Collapse
Affiliation(s)
- Steven Verbruggen
- BioBix, Lab of Bioinformatics and Computational Genomics, Department of Mathematical Modeling, Statistics and Bioinformatics, Faculty of Bioscience Engineering, Ghent University, Ghent, Belgium.
| | - Elvis Ndah
- BioBix, Lab of Bioinformatics and Computational Genomics, Department of Mathematical Modeling, Statistics and Bioinformatics, Faculty of Bioscience Engineering, Ghent University, Ghent, Belgium; VIB-UGent Center for Medical Biotechnology, Ghent, Belgium
| | - Wim Van Criekinge
- BioBix, Lab of Bioinformatics and Computational Genomics, Department of Mathematical Modeling, Statistics and Bioinformatics, Faculty of Bioscience Engineering, Ghent University, Ghent, Belgium
| | - Siegfried Gessulat
- Chair of Proteomics and Bioanalytics, Technical University of Munich, Munich, Germany; SAP SE, Potsdam, Germany
| | - Bernhard Kuster
- Chair of Proteomics and Bioanalytics, Technical University of Munich, Munich, Germany
| | - Mathias Wilhelm
- Chair of Proteomics and Bioanalytics, Technical University of Munich, Munich, Germany
| | - Petra Van Damme
- VIB-UGent Center for Medical Biotechnology, Ghent, Belgium; Department of Biochemistry and Microbiology, Faculty of Sciences, Ghent University, Ghent, Belgium
| | - Gerben Menschaert
- BioBix, Lab of Bioinformatics and Computational Genomics, Department of Mathematical Modeling, Statistics and Bioinformatics, Faculty of Bioscience Engineering, Ghent University, Ghent, Belgium.
| |
Collapse
|
29
|
Perrar A, Dissmeyer N, Huesgen PF. New beginnings and new ends: methods for large-scale characterization of protein termini and their use in plant biology. JOURNAL OF EXPERIMENTAL BOTANY 2019; 70:2021-2038. [PMID: 30838411 PMCID: PMC6460961 DOI: 10.1093/jxb/erz104] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/19/2018] [Accepted: 02/27/2019] [Indexed: 05/17/2023]
Abstract
Dynamic regulation of protein function and abundance plays an important role in virtually every aspect of plant life. Diversifying mechanisms at the RNA and protein level result in many protein molecules with distinct sequence and modification, termed proteoforms, arising from a single gene. Distinct protein termini define proteoforms arising from translation of alternative transcripts, use of alternative translation initiation sites, and different co- and post-translational modifications of the protein termini. Also site-specific proteolytic processing by endo- and exoproteases generates truncated proteoforms, defined by distinct protease-generated neo-N- and neo-C-termini, that may exhibit altered activity, function, and localization compared with their precursor proteins. In eukaryotes, the N-degron pathway targets cytosolic proteins, exposing destabilizing N-terminal amino acids and/or destabilizing N-terminal modifications for proteasomal degradation. This enables rapid and selective removal not only of unfolded proteins, but also of substrate proteoforms generated by proteolytic processing or changes in N-terminal modifications. Here we summarize current protocols enabling proteome-wide analysis of protein termini, which have provided important new insights into N-terminal modifications and protein stability determinants, protein maturation pathways, and protease-substrate relationships in plants.
Collapse
Affiliation(s)
- Andreas Perrar
- Forschungszentrum Jülich, Central Institute for Engineering, Electronics and Analytics, ZEA-3 Analytics, Jülich, Germany
| | - Nico Dissmeyer
- Independent Junior Research Group on Protein Recognition and Degradation, Leibniz Institute of Plant Biochemistry (IPB), Weinberg, Halle (Saale), Germany
- ScienceCampus Halle – Plant-based Bioeconomy, Halle (Saale), Germany
| | - Pitter F Huesgen
- Forschungszentrum Jülich, Central Institute for Engineering, Electronics and Analytics, ZEA-3 Analytics, Jülich, Germany
- Medical Faculty and University Hospital, University of Cologne, Cologne, Germany
| |
Collapse
|
30
|
Stael S, Van Breusegem F, Gevaert K, Nowack MK. Plant proteases and programmed cell death. JOURNAL OF EXPERIMENTAL BOTANY 2019; 70:1991-1995. [PMID: 31222306 PMCID: PMC6460956 DOI: 10.1093/jxb/erz126] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/01/2023]
Affiliation(s)
- Simon Stael
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
- VIB-UGent Center for Plant Systems Biology, Ghent, Belgium
- Department of Biomolecular Medicine, Ghent University, Ghent, Belgium
- VIB-UGent Center for Medical Biotechnology, Ghent, Belgium
| | - Frank Van Breusegem
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
- VIB-UGent Center for Plant Systems Biology, Ghent, Belgium
| | - Kris Gevaert
- Department of Biomolecular Medicine, Ghent University, Ghent, Belgium
- VIB-UGent Center for Medical Biotechnology, Ghent, Belgium
| | - Moritz K Nowack
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
- VIB-UGent Center for Plant Systems Biology, Ghent, Belgium
| |
Collapse
|
31
|
Rendleman J, Choi H, Vogel C. Integration of large-scale multi-omic datasets: a protein-centric view. ACTA ACUST UNITED AC 2018; 11:74-81. [PMID: 30906903 DOI: 10.1016/j.coisb.2018.09.001] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
Innovative mass spectrometry-based proteomics has enabled routine measurements of protein abundance, localization, interactions, and modifications, covering unique aspects of gene expression regulation and function. It is now time to move from isolated analyses of these datasets toward true integration of proteomics with other data types to gain insights from the interactions and interdependencies of biomolecules. When combined with genomic or transcriptomic data, proteomics expands genome annotation to identify variant or missing genes. Dynamic proteomic measurements can move analysis from predominantly concentration-based framework to that of synthesis and degradation of proteins. Proteomic data from thousands of cancer patients can foster identification of novel pathogenic mutations via detection of protein sequence changes that lead to dysregulated pathways in various tumors. Such comprehensive efforts can exploit the synergy arising from large and complex datasets to advance virtually every field of biology.
Collapse
Affiliation(s)
- Justin Rendleman
- Center for Genomics and Systems Biology, New York University, Department of Biology, New York, USA
| | - Hyungwon Choi
- Department of Medicine, Yong Loo Lin School of Medicine, National University Singapore, Singapore.,Institute of Molecular and Cell Biology, Agency for Science, Technology, and Research, Singapore
| | - Christine Vogel
- Center for Genomics and Systems Biology, New York University, Department of Biology, New York, USA
| |
Collapse
|
32
|
Hücker SM, Vanderhaeghen S, Abellan-Schneyder I, Scherer S, Neuhaus K. The Novel Anaerobiosis-Responsive Overlapping Gene ano Is Overlapping Antisense to the Annotated Gene ECs2385 of Escherichia coli O157:H7 Sakai. Front Microbiol 2018; 9:931. [PMID: 29867840 PMCID: PMC5960689 DOI: 10.3389/fmicb.2018.00931] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2018] [Accepted: 04/23/2018] [Indexed: 12/26/2022] Open
Abstract
Current notion presumes that only one protein is encoded at a given bacterial genetic locus. However, transcription and translation of an overlapping open reading frame (ORF) of 186 bp length were discovered by RNAseq and RIBOseq experiments. This ORF is almost completely embedded in the annotated L,D-transpeptidase gene ECs2385 of Escherichia coli O157:H7 Sakai in the antisense reading frame -3. The ORF is transcribed as part of a bicistronic mRNA, which includes the annotated upstream gene ECs2384, encoding a murein lipoprotein. The transcriptional start site of the operon resides 38 bp upstream of the ECs2384 start codon and is driven by a predicted σ70 promoter, which is constitutively active under different growth conditions. The bicistronic operon contains a ρ-independent terminator just upstream of the novel gene, significantly decreasing its transcription. The novel gene can be stably expressed as an EGFP-fusion protein and a translationally arrested mutant of ano, unable to produce the protein, shows a growth advantage in competitive growth experiments compared to the wild type under anaerobiosis. Therefore, the novel antisense overlapping gene is named ano (anaerobiosis responsive overlapping gene). A phylostratigraphic analysis indicates that ano originated very recently de novo by overprinting after the Escherichia/Shigella clade separated from other enterobacteria. Therefore, ano is one of the very rare cases of overlapping genes known in the genus Escherichia.
Collapse
Affiliation(s)
- Sarah M Hücker
- Chair for Microbial Ecology, Technical University of Munich, Freising, Germany
| | - Sonja Vanderhaeghen
- Chair for Microbial Ecology, Technical University of Munich, Freising, Germany
| | | | - Siegfried Scherer
- Chair for Microbial Ecology, Technical University of Munich, Freising, Germany.,Institute for Food & Health, Technical University of Munich, Freising, Germany
| | - Klaus Neuhaus
- Chair for Microbial Ecology, Technical University of Munich, Freising, Germany.,Core Facility Microbiome/NGS, Institute for Food & Health, Technical University of Munich, Freising, Germany
| |
Collapse
|
33
|
Zhang H, Gannon L, Hassall KL, Deery MJ, Gibbs DJ, Holdsworth MJ, van der Hoorn RAL, Lilley KS, Theodoulou FL. N-terminomics reveals control of Arabidopsis seed storage proteins and proteases by the Arg/N-end rule pathway. THE NEW PHYTOLOGIST 2018; 218:1106-1126. [PMID: 29168982 PMCID: PMC5947142 DOI: 10.1111/nph.14909] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/06/2017] [Accepted: 10/23/2017] [Indexed: 05/04/2023]
Abstract
The N-end rule pathway of targeted protein degradation is an important regulator of diverse processes in plants but detailed knowledge regarding its influence on the proteome is lacking. To investigate the impact of the Arg/N-end rule pathway on the proteome of etiolated seedlings, we used terminal amine isotopic labelling of substrates with tandem mass tags (TMT-TAILS) for relative quantification of N-terminal peptides in prt6, an Arabidopsis thaliana N-end rule mutant lacking the E3 ligase PROTEOLYSIS6 (PRT6). TMT-TAILS identified over 4000 unique N-terminal peptides representing c. 2000 protein groups. Forty-five protein groups exhibited significantly increased N-terminal peptide abundance in prt6 seedlings, including cruciferins, major seed storage proteins, which were regulated by Group VII Ethylene Response Factor (ERFVII) transcription factors, known substrates of PRT6. Mobilisation of endosperm α-cruciferin was delayed in prt6 seedlings. N-termini of several proteases were downregulated in prt6, including RD21A. RD21A transcript, protein and activity levels were downregulated in a largely ERFVII-dependent manner. By contrast, cathepsin B3 protein and activity were upregulated by ERFVIIs independent of transcript. We propose that the PRT6 branch of the pathway regulates protease activities in a complex manner and optimises storage reserve mobilisation in the transition from seed to seedling via control of ERFVII action.
Collapse
Affiliation(s)
- Hongtao Zhang
- Plant Sciences DepartmentRothamsted ResearchHarpendenAL5 2JQUK
- Cambridge Centre for ProteomicsDepartment of Biochemistry and Cambridge Systems Biology CentreUniversity of CambridgeCambridge, CB2 1QRUK
| | - Lucy Gannon
- Plant Sciences DepartmentRothamsted ResearchHarpendenAL5 2JQUK
| | - Kirsty L. Hassall
- Computational and Analytical Sciences DepartmentRothamsted ResearchHarpendenAL5 2JQUK
| | - Michael J. Deery
- Cambridge Centre for ProteomicsDepartment of Biochemistry and Cambridge Systems Biology CentreUniversity of CambridgeCambridge, CB2 1QRUK
| | - Daniel J. Gibbs
- School of BiosciencesUniversity of BirminghamEdgbastonB15 2TTUK
| | | | | | - Kathryn S. Lilley
- Cambridge Centre for ProteomicsDepartment of Biochemistry and Cambridge Systems Biology CentreUniversity of CambridgeCambridge, CB2 1QRUK
| | | |
Collapse
|
34
|
Brunet MA, Levesque SA, Hunting DJ, Cohen AA, Roucou X. Recognition of the polycistronic nature of human genes is critical to understanding the genotype-phenotype relationship. Genome Res 2018; 28:609-624. [PMID: 29626081 PMCID: PMC5932603 DOI: 10.1101/gr.230938.117] [Citation(s) in RCA: 42] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2017] [Accepted: 03/27/2018] [Indexed: 12/12/2022]
Abstract
Technological advances promise unprecedented opportunities for whole exome sequencing and proteomic analyses of populations. Currently, data from genome and exome sequencing or proteomic studies are searched against reference genome annotations. This provides the foundation for research and clinical screening for genetic causes of pathologies. However, current genome annotations substantially underestimate the proteomic information encoded within a gene. Numerous studies have now demonstrated the expression and function of alternative (mainly small, sometimes overlapping) ORFs within mature gene transcripts. This has important consequences for the correlation of phenotypes and genotypes. Most alternative ORFs are not yet annotated because of a lack of evidence, and this absence from databases precludes their detection by standard proteomic methods, such as mass spectrometry. Here, we demonstrate how current approaches tend to overlook alternative ORFs, hindering the discovery of new genetic drivers and fundamental research. We discuss available tools and techniques to improve identification of proteins from alternative ORFs and finally suggest a novel annotation system to permit a more complete representation of the transcriptomic and proteomic information contained within a gene. Given the crucial challenge of distinguishing functional ORFs from random ones, the suggested pipeline emphasizes both experimental data and conservation signatures. The addition of alternative ORFs in databases will render identification less serendipitous and advance the pace of research and genomic knowledge. This review highlights the urgent medical and research need to incorporate alternative ORFs in current genome annotations and thus permit their inclusion in hypotheses and models, which relate phenotypes and genotypes.
Collapse
Affiliation(s)
- Marie A Brunet
- Biochemistry Department, Université de Sherbrooke, Quebec J1E 4K8, Canada.,Groupe de recherche PRIMUS, Department of Family and Emergency Medicine, Quebec J1H 5N4, Canada.,PROTEO, Quebec Network for Research on Protein Function, Structure, and Engineering, Université Laval, Quebec G1V 0A6, Canada
| | - Sébastien A Levesque
- Pediatric Department, Centre Hospitalier de l'Université de Sherbrooke, Quebec J1H 5N4, Canada
| | - Darel J Hunting
- Department of Nuclear Medicine & Radiobiology, Université de Sherbrooke, Quebec J1H 5N4, Canada
| | - Alan A Cohen
- Groupe de recherche PRIMUS, Department of Family and Emergency Medicine, Quebec J1H 5N4, Canada
| | - Xavier Roucou
- Biochemistry Department, Université de Sherbrooke, Quebec J1E 4K8, Canada.,PROTEO, Quebec Network for Research on Protein Function, Structure, and Engineering, Université Laval, Quebec G1V 0A6, Canada
| |
Collapse
|
35
|
Hücker SM, Vanderhaeghen S, Abellan-Schneyder I, Wecko R, Simon S, Scherer S, Neuhaus K. A novel short L-arginine responsive protein-coding gene (laoB) antiparallel overlapping to a CadC-like transcriptional regulator in Escherichia coli O157:H7 Sakai originated by overprinting. BMC Evol Biol 2018; 18:21. [PMID: 29433444 PMCID: PMC5810103 DOI: 10.1186/s12862-018-1134-0] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2017] [Accepted: 01/31/2018] [Indexed: 11/10/2022] Open
Abstract
Background Due to the DNA triplet code, it is possible that the sequences of two or more protein-coding genes overlap to a large degree. However, such non-trivial overlaps are usually excluded by genome annotation pipelines and, thus, only a few overlapping gene pairs have been described in bacteria. In contrast, transcriptome and translatome sequencing reveals many signals originated from the antisense strand of annotated genes, of which we analyzed an example gene pair in more detail. Results A small open reading frame of Escherichia coli O157:H7 strain Sakai (EHEC), designated laoB (L-arginine responsive overlapping gene), is embedded in reading frame −2 in the antisense strand of ECs5115, encoding a CadC-like transcriptional regulator. This overlapping gene shows evidence of transcription and translation in Luria-Bertani (LB) and brain-heart infusion (BHI) medium based on RNA sequencing (RNAseq) and ribosomal-footprint sequencing (RIBOseq). The transcriptional start site is 289 base pairs (bp) upstream of the start codon and transcription termination is 155 bp downstream of the stop codon. Overexpression of LaoB fused to an enhanced green fluorescent protein (EGFP) reporter was possible. The sequence upstream of the transcriptional start site displayed strong promoter activity under different conditions, whereas promoter activity was significantly decreased in the presence of L-arginine. A strand-specific translationally arrested mutant of laoB provided a significant growth advantage in competitive growth experiments in the presence of L-arginine compared to the wild type, which returned to wild type level after complementation of laoB in trans. A phylostratigraphic analysis indicated that the novel gene is restricted to the Escherichia/Shigella clade and might have originated recently by overprinting leading to the expression of part of the antisense strand of ECs5115. Conclusions Here, we present evidence of a novel small protein-coding gene laoB encoded in the antisense frame −2 of the annotated gene ECs5115. Clearly, laoB is evolutionarily young and it originated in the Escherichia/Shigella clade by overprinting, a process which may cause the de novo evolution of bacterial genes like laoB. Electronic supplementary material The online version of this article (10.1186/s12862-018-1134-0) contains supplementary material, which is available to authorized users.
Collapse
Affiliation(s)
- Sarah M Hücker
- Chair for Microbial Ecology, Wissenschaftszentrum Weihenstephan, Technische Universität München, Weihenstephaner Berg 3, 85354, Freising, Germany.,Fraunhofer ITEM-R, Am Biopark 9, 93053, Regensburg, Germany
| | - Sonja Vanderhaeghen
- Chair for Microbial Ecology, Wissenschaftszentrum Weihenstephan, Technische Universität München, Weihenstephaner Berg 3, 85354, Freising, Germany
| | - Isabel Abellan-Schneyder
- Chair for Microbial Ecology, Wissenschaftszentrum Weihenstephan, Technische Universität München, Weihenstephaner Berg 3, 85354, Freising, Germany.,Core Facility Microbiome/NGS, ZIEL - Institute for Food & Health, Technische Universität München, Weihenstephaner Berg 3, 85354, Freising, Germany
| | - Romy Wecko
- Chair for Microbial Ecology, Wissenschaftszentrum Weihenstephan, Technische Universität München, Weihenstephaner Berg 3, 85354, Freising, Germany
| | - Svenja Simon
- Department of Computer and Information Science, University of Konstanz, Box 78, 78457, Konstanz, Germany
| | - Siegfried Scherer
- Chair for Microbial Ecology, Wissenschaftszentrum Weihenstephan, Technische Universität München, Weihenstephaner Berg 3, 85354, Freising, Germany.,ZIEL - Institute for Food & Health, Technische Universität München, Weihenstephaner Berg 3, 85354, Freising, Germany
| | - Klaus Neuhaus
- Chair for Microbial Ecology, Wissenschaftszentrum Weihenstephan, Technische Universität München, Weihenstephaner Berg 3, 85354, Freising, Germany. .,Core Facility Microbiome/NGS, ZIEL - Institute for Food & Health, Technische Universität München, Weihenstephaner Berg 3, 85354, Freising, Germany.
| |
Collapse
|
36
|
Na CH, Barbhuiya MA, Kim MS, Verbruggen S, Eacker SM, Pletnikova O, Troncoso JC, Halushka MK, Menschaert G, Overall CM, Pandey A. Discovery of noncanonical translation initiation sites through mass spectrometric analysis of protein N termini. Genome Res 2017; 28:25-36. [PMID: 29162641 PMCID: PMC5749180 DOI: 10.1101/gr.226050.117] [Citation(s) in RCA: 57] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2017] [Accepted: 11/16/2017] [Indexed: 12/29/2022]
Abstract
Translation initiation generally occurs at AUG codons in eukaryotes, although it has been shown that non-AUG or noncanonical translation initiation can also occur. However, the evidence for noncanonical translation initiation sites (TISs) is largely indirect and based on ribosome profiling (Ribo-seq) studies. Here, using a strategy specifically designed to enrich N termini of proteins, we demonstrate that many human proteins are translated at noncanonical TISs. The large majority of TISs that mapped to 5′ untranslated regions were noncanonical and led to N-terminal extension of annotated proteins or translation of upstream small open reading frames (uORF). It has been controversial whether the amino acid corresponding to the start codon is incorporated at the TIS or methionine is still incorporated. We found that methionine was incorporated at almost all noncanonical TISs identified in this study. Comparison of the TISs determined through mass spectrometry with ribosome profiling data revealed that about two-thirds of the novel annotations were indeed supported by the available ribosome profiling data. Sequence conservation across species and a higher abundance of noncanonical TISs than canonical ones in some cases suggests that the noncanonical TISs can have biological functions. Overall, this study provides evidence of protein translation initiation at noncanonical TISs and argues that further studies are required for elucidation of functional implications of such noncanonical translation initiation.
Collapse
Affiliation(s)
- Chan Hyun Na
- McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland 21205, USA.,Department of Neurology, Johns Hopkins University School of Medicine, Baltimore, Maryland 21205, USA.,Institute for Cell Engineering, Johns Hopkins University School of Medicine, Baltimore, Maryland 21205, USA
| | - Mustafa A Barbhuiya
- McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland 21205, USA.,Department of Neurology, Johns Hopkins University School of Medicine, Baltimore, Maryland 21205, USA
| | - Min-Sik Kim
- Department of Biological Chemistry, Johns Hopkins University School of Medicine, Baltimore, Maryland 21205, USA.,Department of Applied Chemistry, College of Applied Science, Kyung Hee University, Yongin, 446-701 Korea
| | - Steven Verbruggen
- Lab of Bioinformatics and Computational Genomics (BioBix), Department of Mathematical Modeling, Statistics and Bioinformatics, Faculty of Bioscience Engineering, Ghent University, 9000 Ghent, Belgium
| | - Stephen M Eacker
- Department of Neurology, Johns Hopkins University School of Medicine, Baltimore, Maryland 21205, USA.,Institute for Cell Engineering, Johns Hopkins University School of Medicine, Baltimore, Maryland 21205, USA
| | - Olga Pletnikova
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, Maryland 21287, USA
| | - Juan C Troncoso
- Department of Neurology, Johns Hopkins University School of Medicine, Baltimore, Maryland 21205, USA.,Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, Maryland 21287, USA
| | - Marc K Halushka
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, Maryland 21287, USA
| | - Gerben Menschaert
- Department of Applied Chemistry, College of Applied Science, Kyung Hee University, Yongin, 446-701 Korea
| | - Christopher M Overall
- Department of Biochemistry and Molecular Biology, Life Sciences Institute, University of British Columbia, Vancouver, British Columbia V6T 1Z3, Canada
| | - Akhilesh Pandey
- McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland 21205, USA.,Institute for Cell Engineering, Johns Hopkins University School of Medicine, Baltimore, Maryland 21205, USA.,Department of Biological Chemistry, Johns Hopkins University School of Medicine, Baltimore, Maryland 21205, USA.,Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, Maryland 21287, USA.,Department of Oncology, Johns Hopkins University School of Medicine, Baltimore, Maryland 21287, USA
| |
Collapse
|
37
|
Starr AE, Deeke SA, Li L, Zhang X, Daoud R, Ryan J, Ning Z, Cheng K, Nguyen LVH, Abou-Samra E, Lavallée-Adam M, Figeys D. Proteomic and Metaproteomic Approaches to Understand Host–Microbe Interactions. Anal Chem 2017; 90:86-109. [DOI: 10.1021/acs.analchem.7b04340] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Affiliation(s)
- Amanda E. Starr
- Ottawa Institute of Systems Biology and Department of Biochemistry, Microbiology and Immunology, University of Ottawa, Ottawa, Ontario, K1N 6N5, Canada
| | - Shelley A. Deeke
- Ottawa Institute of Systems Biology and Department of Biochemistry, Microbiology and Immunology, University of Ottawa, Ottawa, Ontario, K1N 6N5, Canada
| | - Leyuan Li
- Ottawa Institute of Systems Biology and Department of Biochemistry, Microbiology and Immunology, University of Ottawa, Ottawa, Ontario, K1N 6N5, Canada
| | - Xu Zhang
- Ottawa Institute of Systems Biology and Department of Biochemistry, Microbiology and Immunology, University of Ottawa, Ottawa, Ontario, K1N 6N5, Canada
| | - Rachid Daoud
- Ottawa Institute of Systems Biology and Department of Biochemistry, Microbiology and Immunology, University of Ottawa, Ottawa, Ontario, K1N 6N5, Canada
| | - James Ryan
- Ottawa Institute of Systems Biology and Department of Biochemistry, Microbiology and Immunology, University of Ottawa, Ottawa, Ontario, K1N 6N5, Canada
| | - Zhibin Ning
- Ottawa Institute of Systems Biology and Department of Biochemistry, Microbiology and Immunology, University of Ottawa, Ottawa, Ontario, K1N 6N5, Canada
| | - Kai Cheng
- Ottawa Institute of Systems Biology and Department of Biochemistry, Microbiology and Immunology, University of Ottawa, Ottawa, Ontario, K1N 6N5, Canada
| | - Linh V. H. Nguyen
- Ottawa Institute of Systems Biology and Department of Biochemistry, Microbiology and Immunology, University of Ottawa, Ottawa, Ontario, K1N 6N5, Canada
| | - Elias Abou-Samra
- Ottawa Institute of Systems Biology and Department of Biochemistry, Microbiology and Immunology, University of Ottawa, Ottawa, Ontario, K1N 6N5, Canada
| | - Mathieu Lavallée-Adam
- Ottawa Institute of Systems Biology and Department of Biochemistry, Microbiology and Immunology, University of Ottawa, Ottawa, Ontario, K1N 6N5, Canada
| | - Daniel Figeys
- Ottawa Institute of Systems Biology and Department of Biochemistry, Microbiology and Immunology, University of Ottawa, Ottawa, Ontario, K1N 6N5, Canada
- Department of Chemistry and Biomolecular Sciences, University of Ottawa, Ottawa, Ontario, K1N 6N5, Canada
- Molecular Architecture of Life Program, Canadian Institute for Advanced Research, Toronto, Ontario, M5G 1M1, Canada
| |
Collapse
|
38
|
Beyond Read-Counts: Ribo-seq Data Analysis to Understand the Functions of the Transcriptome. Trends Genet 2017; 33:728-744. [PMID: 28887026 DOI: 10.1016/j.tig.2017.08.003] [Citation(s) in RCA: 79] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2017] [Revised: 08/03/2017] [Accepted: 08/04/2017] [Indexed: 01/16/2023]
Abstract
By mapping the positions of millions of translating ribosomes in the cell, ribosome profiling (Ribo-seq) has established its role as a powerful tool to study gene expression. Several laboratories have introduced modifications to the experimental protocol and expanded the repertoire of biochemical methods to study translation transcriptome-wide. However, the diversity of protocols highlights a need for standardization. At the same time, different computational analysis strategies have used Ribo-seq data to identify the set of translated sequences with high confidence. In this review we present an overview of such methodologies, outlining their assumptions, data requirements, and availability. At the interface between RNA and proteins, Ribo-seq can complement data from multiple omics approaches, zooming in on the central role of translation in the molecular cell.
Collapse
|